.\" Automatically generated by Pandoc 2.14.0.3
.\"
.TH "PLOTHAPS" "1" "" "plotHaps (vcflib)" "plotHaps (VCF statistics)"
.hy
.SH NAME
.PP
\f[B]plotHaps\f[R]
.SH SYNOPSIS
.SH DESCRIPTION
.PP
\f[B]plotHaps\f[R] provides the formatted output that can be used with
`bin/plotHaplotypes.R'.
.SH OPTIONS
.IP
.nf
\f[C]

Output : haplotype matrix and positions

**plotHaps**  --target 0,1,2,3,4,5,6,7  --file my.phased.vcf.gz                                                           

required: t,target     -- argument: a zero base comma separated list of target individuals corrisponding to VCF column s        
required: r,region     -- argument: a tabix compliant genomic range : \[dq]seqid:start-end\[dq] or \[dq]seqid\[dq]                          
required: f,file       -- argument: proper formatted phased VCF file                                                            
required: y,type       -- argument: genotype likelihood format: PL,GP,GP                                                        

Type: statistics
\f[R]
.fi
.SH EXIT VALUES
.TP
\f[B]0\f[R]
Success
.TP
\f[B]not 0\f[R]
Failure
.SH SEE ALSO
.PP
\f[B]vcflib\f[R](1)
.SH OTHER
.SH LICENSE
.PP
Copyright 2011-2023 (C) Erik Garrison and vcflib contributors.
MIT licensed.
.SH AUTHORS
Erik Garrison and vcflib contributors.